Equine Genetics 101: Genetic Concepts and Applications

Even for the most knowledgeable horseman, equine genetics can be a confusing topic to grasp. Trying to conceptualize how genetics can be applied to equine performance can be even more confusing. But the attendees at the 2011 Thoroughbred Pedigree, Genetics, and Performance Conference, held Sept. 7-8 in Lexington, Ky., were in luck as Jamie MacLeod, VMD, PhD, and Ernie Bailey, PhD, presented an overview of equine genetics and the different applications they have in equine performance.

MacLeod began by confirming that there is, in fact, a link between genetics and performance in horses. Genetics is the basis of selective breeding programs, and it's generally the point upon which the financial value of bloodstock is based, he explained.

"Selecting parents (sire and dam) that hopefully will pass superior genetic determinants to their offspring (foal) represents the planned breeding strategy we use to enhance our chances of producing a truly outstanding individual," he added.

In producing an equine athlete, MacLeod explained, while a large number of genetic variables are involved in "something as complex as the performance of a racehorse," the equally large number of nongenetic variables, such as environmental factors, also influence the ability--or inability--of a horse to reach his or her peak athletic potential.

"Is everything figured out?" he asked. "Absolutely not. There is so much more to learn about. Understanding the role of inherited genetic determinants in health and performance are very active areas of scientific research."

The Basics

MacLeod explained that one of the limiting factors in most horse people's understanding of genetics is the terminology researchers use to discuss it. So to help attendees better understand the rest of the presentations they would encounter throughout the conference, MacLeod reviewed some of the basic terms often used in equine genetics discussions.

"The central dogma of gene expression," as MacLeod described it, is simply the functional relationship between deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein.

"DNA serves as a template for its own replication and for the transcription (more on that in a moment) of RNA which, in turn, is translated into protein," MacLeod explained in the program notes.

DNA--Deoxyribosenucleic acid is the molecule containing genetic information passed from parent to offspring. Four nucleotide bases--adenine, guanine, thymine, and cytosine--make up all species' DNA; however, how it is organized remains unique to each particular species with additional variation between individuals. Nucleotides are usually abbreviated using their first letters (adenine, for example, is referred to as "A") and only pair with certain other base pairs (adenine pairs with thymine and guanine pairs with cytosine to form the DNA double helix, or twisted ladder, shape).

The DNA is located within the nucleus of a cell, MacLeod explained, and is structurally organized rather than just randomly distributed.

Genome--The "total endowment" of an organism's DNA is referred to as the genome, MacLeod said. The equine genome, for which the sequence was completed in 2007, contains about 2.7 billion nucleotide base pairs and has about 21,000 protein coding genes. (More on the genome in a minute.)

Genes--These discreet segments of the genomic DNA encode functional RNA or protein products. The key concept is that genes are "functional units of DNA," responsible for the inherited traits we observe in an individual, MacLeod said. He explained that genes have two broad functional parts:

The coding region of the gene contains DNA bases that are expressed to generate the functional gene product ("The part that makes the protein that we all think about in terms of regulating the trait," MacLeod said); or

The regulatory elements of the gene that control when, where, and how much a gene is expressed.

"These regulatory elements and the coding region work in a coordinated fashion in health, but if either part gets changed or reorganized, the gene's functional properties can be altered," MacLeod added.

Transcription--MacLeod then described the concept of transcription, which is "the process of synthesizing RNA as specified by the DNA template of a gene's coding region." Regulatory elements of a gene determine, when, where, and how much a gene is transcribed, and all transcriptional processes are localized in the cell's nucleus, he noted.

Translation--Not to be confused with transcription, translation is the process that produces a protein and occurs outside of the nucleus in the cell's cytoplasm.

Transcription converts the genetic information from DNA to RNA. Translation is when the base sequence of the RNA directs the formation of a defined linear order of amino acids to generate a specific protein, MacLeod said.

"For protein-coding genes, the protein is what regulates the trait we're interested in studying," he added.

One of the classic strategies is to consider one or several candidate genes, which often are identified from other research studies conducted by another scientist, he said. If a gene has been shown to be important in what appears to be a similar trait in other species (such as humans, dogs, cattle, or mice), it could also be relevant in the horse.

"This approach has worked in equine science, but for many traits we don't have a good candidate gene or perhaps want to consider other possibilities as well," MacLeod said. "Now we can use unbiased genomic screens to identify important genes for a trait or other phenotype (physical characteristic) of interest in the horse."

These scans typically utilize genetic arrays or gene chips, which MacLeod described as "devices used by scientists to investigate a large set of nucleotide sequences." Very simply put, the arrays and gene chips are tools that stemmed from the complete sequencing of the equine genome. They enable researchers to examine all of the genes at once in an attempt to find gene(s) regulating a trait of interest.

From there, MacLeod explained that differences in the genomic DNA sequence between individual horses that are called single nucleotide polymorphisms, or SNPs, are now commonly profiled on gene chips for genomic scans (in other species). In the notes, MacLeod explained that SNPs are "the smallest and most common type of genetic variant: the alteration of a single base of DNA from one nucleotide to another between individuals."

He explained that SNPs are distributed across the genome and inherited from the parents to the offspring. Through an analytical technique called Genome-Wide Association Study (GWAS), scientists can use SNPs to localize a specific region of the genome that appears to contain important genetic determinants for the trait being studied. In other words, the GWAS data can reduce the magnitude of the research challenge substantially by identifying a region of the genome that should be investigated further, focusing interest on just a few protein-coding genes from what was originally the full set of approximately 21,000 across equine genome, MacLeod said.

Bailey then took the stage to discuss some of genetics' current practical applications. For example, he explained that the origin (or the genetics) of the Thoroughbred horse can be traced back over 300 years. Paddy Cunningham, PhD, professor emeritus at Trinity College in Dublin, Ireland, published an article in 2001 that described the contribution of the foundation horses (defined as those foaled before 1750 and of unknown lineage) to the breed, he explained.

A total of 158 horses were considered "founders" of the Thoroughbred breed, including 85 males and 73 females. Of course, as most Thoroughbred enthusiasts know, the three main sires to which all Thoroughbreds can trace their "tail-male" lineage are the Godolphin Arabian, the Darley Arabian, and the Byerley Turk.

"That precisely defines the source of the Y chromosome for horses," Bailey explained. "Ninety-five percent of Thoroughbred stallions are descended from the Darley Arabian, and consequently, they all have the Y chromosome of that founder."

The human Y chromosome contains about 86 genes, Bailey said, and the equine counterpart contains a similar number.

Bailey then explained that the "tail-female" line identifies the inheritance of the mitochondria, which are responsible for generating energy in the cells. Mitochondria are inherited only from the dam, and the modern day mitochondria are descended from the foundation mares. Mitochondria in horses contain 37 genes; however, most of the genes responsible for the mitochondria's structure and function are found on chromosomes, Bailey said, adding that this is the same location at which the remainder of the 20,322 genes are found.

"Cunningham also studied the overall contribution of each founder to the genetics of modern horses and found that the most significant contributor was actually the Goldolphin Arabian, which contributed 13.8% of all the genes, on average, in the modern Thoroughbred," Bailey explained. "The next highest contributor was the Darley Arabian, with 6.5%. This means that the most significant founder of the Thoroughbred breed was the Goldophin Arabian when considering the entire genetic profile. At the same time it shows that Thoroughbred horses are not clonal animals (those that descended from and are genetically identical to a single common ancestor) and there is lots of genetic diversity based on the pedigree."

Bailey reported that the first horse genome was completed for a Thoroughbred mare named Twilight, a resident of Cornell University in Ithaca, N.Y. Twilight's genome sequence shed light on more than one million different genetic variants (or SNPs). A total of 20,322 genes were predicted at the time, and a frequency of 1 SNP per 1,050 base pairs was estimated, he said.

The DNA sequences also allowed scientists to compare the amount of genetic variation (genetic complexity) among several species. Researchers have also found that horses have a more complex genome than dogs, but a less complex genome than humans. Bailey explained that this shows horses have a large amount of genetic variation for breeders to work with.

"It also means that we can make discoveries with more simple tools than required for human studies," Bailey added.

He then reviewed some of the different methods by which genetic mutations can be studied:

Family studies, he explained, are beneficial but difficult to facilitate as families of horses are "tough to keep as laboratory animals";

Candidate gene studies have been helpful in picking up new diseases and mutations, he explained, adding that in some cases predictions have been made from mutations identified on other species; and

Genome-wide association studies are the type many researchers are most excited about. For GWAS studies, scientists do not need families and can investigate tens of thousands of genes and regulatory DNA elements simultaneously.

Bailey concluded by summarizing the current state of equine genetics: "Horse genetics has come a long way in the last 10 years. We have the ability to localize genetic effects for any well-defined trait to a specific region of the genome; we have a list of genes in that area from the analyses of the genome sequence; we can investigate gene expression; and we can also consider gene function in estimating which gene or set of genes are responsible for traits of interest."

He noted that research has revealed horses have "lots of genetic diversity" and has made it possible to "easily identify genes for simple hereditary traits."

Bailey expressed that although genomics has come a long way, there is still work to be done to more easily "identify genes for complex traits (such as athletic potential), to better understand the interplay of gene expression and management practices, and to better understand the complexity of 21,000 interacting genes."

Disclaimer: Seek the advice of a qualified veterinarian before proceeding with any diagnosis, treatment, or therapy.